What I am concerned is how would the ns/day be affected if and if not the
simulations run to the entirety. The mdinfo file states ns/day obtained due
to last 'x' steps, hence if the 'x' = 10000 and not 1000, is there a chance
the average would be better for 10000 steps??
~mayank
On Tue, Aug 17, 2010 at 11:31 AM, Jason Swails <jason.swails.gmail.com>wrote:
> Hello,
>
> I believe that pmemd does not update the mdinfo file as often as it updates
> the mdout file due to performance implications. You can figure out the
> source of this discrepancy by digging through the pmemd code, but this has
> no effect on your results.
>
> Hope this helps,
> Jason
>
> On Tue, Aug 17, 2010 at 11:10 AM, Mayank Daga <mdaga.vt.edu> wrote:
>
> > Hi,
> >
> > I am a newbie using AMBER on the GPUs.
> > When I run my simulations, I see two output files, mdout and mdinfo. In
> the
> > mdinfo file, I see the timing details as to how many ns/day I get. The
> > issue
> > is some steps are always uncompleted according to this file while mdout
> > lists that all the steps have been completed. Why is this discrepancy?
> > For example, if I run a simulation for 10000 steps, mdinfo shows 9000
> steps
> > remaining while mdout list energy values for all 10000 steps.
> >
> > I am using the input files as downloaded from the AMBER website and to
> run
> > the simulation:
> > ~/amber11/bin/pmemd.cuda -O -i mdin -o mdout -p prmtop -c inpcrd -r
> restrt
> > -x mdcrd -gpu 0
> >
> > Please explain this behaviour.
> >
> > Thanks,
> > ~mayank
> >
> >
> > --
> > Mayank Daga | SyNeRGy Laboratory | Dept. of Computer Science
> > Virginia Tech | http://synergy.cs.vt.edu | http://www.cs.vt.edu
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Mayank Daga | SyNeRGy Laboratory | Dept. of Computer Science
Virginia Tech | http://synergy.cs.vt.edu | http://www.cs.vt.edu
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Received on Tue Aug 17 2010 - 09:00:07 PDT
